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Update all subworkflows name #784

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merged 44 commits into from
Oct 13, 2022
Merged

Update all subworkflows name #784

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7dc75bd
move and rename subworkflows
maxulysse Oct 10, 2022
2d4a933
rename all old local modules following new naming convention
maxulysse Oct 11, 2022
6946b58
fix name and path for preprocessing
maxulysse Oct 11, 2022
18e17c2
fix name and path for germline variant calling
maxulysse Oct 11, 2022
1a8d131
fix name and path for tumor only and somatic variant calling
maxulysse Oct 11, 2022
c1d6970
fix name and path for annotation
maxulysse Oct 11, 2022
dd6eda8
fix FASTQC module output
maxulysse Oct 11, 2022
821a72e
more fix on paths
maxulysse Oct 11, 2022
e568ecb
fix pytest for default
maxulysse Oct 11, 2022
c674795
fix annotation pytests
maxulysse Oct 11, 2022
2fe999a
fix controlfreec pytests
maxulysse Oct 11, 2022
6dfe7e6
fixing haplotypecaller pytests
maxulysse Oct 11, 2022
a2f9617
Merge remote-tracking branch 'upstream/dev' into dev_subworkflows
maxulysse Oct 11, 2022
5cc6d72
prettier
maxulysse Oct 11, 2022
e17df48
fix tiddit pytests
maxulysse Oct 11, 2022
f34dfa0
update CHANGELOG
maxulysse Oct 12, 2022
6fec797
Merge remote-tracking branch 'upstream/dev' into dev_subworkflows
maxulysse Oct 12, 2022
874e3e5
update CHANGELOG
maxulysse Oct 12, 2022
f365613
Merge remote-tracking branch 'upstream/dev' into dev_subworkflows
maxulysse Oct 12, 2022
2abe4ee
Merge remote-tracking branch 'upstream/dev' into dev_subworkflows
maxulysse Oct 12, 2022
d187572
fix deleted file
maxulysse Oct 12, 2022
c5aa7c2
remove include BAM_COMPRESS_SAMTOOLS
maxulysse Oct 12, 2022
67927c4
fix default pytests
maxulysse Oct 12, 2022
587a1d3
fix subworkfows inclusion
maxulysse Oct 12, 2022
31ba27e
fix markduplicates
maxulysse Oct 12, 2022
01b3752
fix markduplicates pytests
maxulysse Oct 12, 2022
7b65803
fix save_mapped
maxulysse Oct 12, 2022
5b9283f
fix save_mapped pytests
maxulysse Oct 12, 2022
d04e054
fix deepvariant pytests
maxulysse Oct 12, 2022
cc74a0f
Merge remote-tracking branch 'upstream/dev' into dev_subworkflows
maxulysse Oct 12, 2022
73d696d
fix variant calling
maxulysse Oct 12, 2022
3f29147
fix prettier
maxulysse Oct 12, 2022
83931d3
fix gatk_spark pytests
maxulysse Oct 12, 2022
25f1eda
update checksum
maxulysse Oct 12, 2022
39a65ba
fix freebayes pytests
maxulysse Oct 12, 2022
948a4fa
fix deepvariant checksum
maxulysse Oct 12, 2022
1f110bc
fix more tests
maxulysse Oct 12, 2022
ce1358a
fix save output as bam tests
maxulysse Oct 12, 2022
4c73847
fix skip md tests
maxulysse Oct 12, 2022
1fd5729
fix checksums
maxulysse Oct 12, 2022
c1f8d58
fix BAM_TO_CRAM_MAPPING
maxulysse Oct 12, 2022
595e65f
fix samtools stats output
maxulysse Oct 12, 2022
b4f7ca0
fix MD
maxulysse Oct 12, 2022
779de63
publish files
maxulysse Oct 12, 2022
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0 subworkflows/nf-core/bam_to_cram.nf → ...flows/local/bam_compress_samtools/main.nf
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0 subworkflows/nf-core/alignment_to_fastq.nf → ...kflows/local/bam_convert_samtools/main.nf
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0 ...rkflows/nf-core/gatk4/recalibrate/main.nf → ...orkflows/local/bam_cram_applybqsr/main.nf
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0 ...s/nf-core/gatk4/recalibrate_spark/main.nf → ...ws/local/bam_cram_applybqsr_spark/main.nf
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0 ...-core/gatk4/prepare_recalibration/main.nf → ...s/local/bam_cram_baserecalibrator/main.nf
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0 ...gatk4/prepare_recalibration_spark/main.nf → ...l/bam_cram_baserecalibrator_spark/main.nf
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0 ...k4/joint_germline_variant_calling/main.nf → ..._cram_joint_calling_germline_gatk/main.nf
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0 ...4/joint_germline_variant_calling/meta.yml → ...cram_joint_calling_germline_gatk/meta.yml
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0 ...lows/nf-core/gatk4/markduplicates/main.nf → ...ows/local/bam_cram_markduplicates/main.nf
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0 ...f-core/gatk4/markduplicates_spark/main.nf → ...cal/bam_cram_markduplicates_spark/main.nf
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0 ...lows/nf-core/variantcalling/ascat/main.nf → ...al/bam_cram_variant_calling_ascat/main.nf
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0 ...ows/nf-core/variantcalling/cnvkit/main.nf → ...l/bam_cram_variant_calling_cnvkit/main.nf
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0 ...f-core/variantcalling/deepvariant/main.nf → ..._cram_variant_calling_deepvariant/main.nf
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0 .../nf-core/variantcalling/freebayes/main.nf → ...am_cram_variant_calling_freebayes/main.nf
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0 ...ore/variantcalling/manta/germline/main.nf → ...am_variant_calling_germline_manta/main.nf
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0 ...re/variantcalling/haplotypecaller/main.nf → ...m_variant_calling_haplotypecaller/main.nf
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0 ...ws/nf-core/variantcalling/mpileup/main.nf → .../bam_cram_variant_calling_mpileup/main.nf
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0 ...ore/variantcalling/strelka/single/main.nf → ...am_variant_calling_single_strelka/main.nf
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0 ...core/variantcalling/tiddit/single/main.nf → ...ram_variant_calling_single_tiddit/main.nf
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0 ...riantcalling/controlfreec/somatic/main.nf → ...iant_calling_somatic_controlfreec/main.nf
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0 ...core/variantcalling/manta/somatic/main.nf → ...ram_variant_calling_somatic_manta/main.nf
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0 ...or_normal_somatic_variant_calling/main.nf → ...m_variant_calling_somatic_mutect2/main.nf
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0 ...r_normal_somatic_variant_calling/meta.yml → ..._variant_calling_somatic_mutect2/meta.yml
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0 ...re/variantcalling/strelka/somatic/main.nf → ...m_variant_calling_somatic_strelka/main.nf
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0 ...ore/variantcalling/tiddit/somatic/main.nf → ...am_variant_calling_somatic_tiddit/main.nf
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0 ...antcalling/controlfreec/tumoronly/main.nf → ...t_calling_tumor_only_controlfreec/main.nf
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0 ...re/variantcalling/manta/tumoronly/main.nf → ..._variant_calling_tumor_only_manta/main.nf
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0 ...umor_only_somatic_variant_calling/main.nf → ...ariant_calling_tumor_only_mutect2/main.nf
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0 ...mor_only_somatic_variant_calling/meta.yml → ...riant_calling_tumor_only_mutect2/meta.yml
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0 subworkflows/nf-core/merge_index_bam.nf → ...ws/local/bam_merge_index_samtools/main.nf
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0 subworkflows/nf-core/merge_index_cram.nf → ...s/local/cram_merge_index_samtools/main.nf
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0 subworkflows/nf-core/cram_qc.nf → ...s/local/cram_qc_mosdepth_samtools/main.nf
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0 subworkflows/nf-core/gatk4/mapping/main.nf → ...l/fastq_align_bwamem_mem2_dragmap/main.nf
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0 ...f-core/fgbio_create_umi_consensus/main.nf → .../fastq_create_umi_consensus_fgbio/main.nf
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0 subworkflows/nf-core/run_fastqc.nf → subworkflows/local/fastq_qc_fastqc/main.nf
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0 ...ows/nf-core/annotation/ensemblvep/main.nf → ...ows/local/vcf_annotate_ensemblvep/main.nf
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0 ...ws/nf-core/annotation/ensemblvep/meta.yml → ...ws/local/vcf_annotate_ensemblvep/meta.yml
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0 ...rkflows/nf-core/annotation/snpeff/main.nf → ...rkflows/local/vcf_annotate_snpeff/main.nf
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0 ...kflows/nf-core/annotation/snpeff/meta.yml → ...kflows/local/vcf_annotate_snpeff/meta.yml
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0 subworkflows/nf-core/vcf_qc.nf → ...ws/local/vcf_qc_bcftools_vcftools/main.nf
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0 ...e_sample_germline_variant_calling/main.nf → .../local/vcf_variant_filtering_gatk/main.nf
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